The original intent back in the 1880's was to issue two fitted magazines with the rifle, one chained to the rifle using that loop in the trigger guard and the other to be carried in the soldier's kit or pocket. The reserve magazine was to be used if the regular magazine was damaged or if there was no time to reload it.
That changed with charger loading, and issuing of the extra magazine was discontinued, as was the loop on the magazine for the chain. The loop on the rifle was retained and later used to tie on the receiver cover, which many folks think was the original reason for it. By WWI, all loading was done by chargers ("stripper clips") and the magazine was never removed except for cleaning or replacement.